AMECAFE said output during the cycle will total 3.1 million 60-kg bags.
The association also said the persistence of heavy rain, which presents an ideal environment for the spread of roya, is a major contributing factor to the expected fall in production.
Apart from the new production estimate, AMECAFE added that a survey of coffee farmers' perceptions indicates output during the current cycle could dip even further to 2.7 million bags.
Mexico's southern Chiapas state, the country's main coffee-growing region, is where the largest drop in output is expected. But AMECAFE said parts of five other states are also expected to see reduced yields: Veracruz, Hidalgo, Jalisco, Nayarit and Guerrero.
In October, the national representative of Sistema Producto Cafe, Mexico's main coffee industry association, said as many as 100,000 hectares (247,000 acres) of Chiapas' total planted land, or 40 percent, are dotted with the yellow-orange spores of the deadly plant disease.
Aggressive roya outbreaks in Mexico and each of Central America's five major coffee-producing nations dating back to the previous 2012/2013 season are threatening sharply reduced yields and export revenues across the region.
The coffee season in Central America and Mexico, which together produce more than one-fifth of the world's arabica beans, runs from October through September.